The officials say the rain will intensify from Wednesday. They say some Pacific coastal areas of western and eastern Japan may have localized downpours of more than 80 millimeters per hour.
They say the heavy rain may continue even after the storm moves away, and overall precipitation could reach 1,000 millimeters in some areas.
Many people in Japan are currently taking vacations during the Bon summer holiday period.
Officials are advising the holidaymakers to check the latest updates and to watch for stormy weather, which may bring floods and landslides.
The storm could disrupt transportation systems. Railway operators in western Japan say they may be forced to suspend services on Wednesday and Thursday.
Airlines are also asking passengers to check for flight cancelations. They advise people to check online for updates.